Figure 5: Discrimination basis against near-cognate duplexes with pyrimidine–pyrimidine U·U mismatches in the decoding centre of the 70S ribosome.
(a) Critical A1492 and A1492/G530 of 16S rRNA stabilize the sugar phosphate backbones of the U·U mismatch at the first (left) and second (right) positions of the codon–anticodon duplex by A-minor groove interactions as is the case for any canonical Watson–Crick pair29,30. 2Fo−Fc electron density maps are contoured at 1.5σ. (b,c) Geometries of the U·U mismatch at the first (b) and second (c) positions of the codon anticodon duplex; van der Waals surfaces (left) together with interatomic distances (right) are presented. In b, the table describes standard categories of hydrogen bonds. (d) Formation of a strong U·U pair would necessitate a shift in the keto-enol equilibrium from abundant keto form (left panel) to a rare enol form (red frame) and the 3-Å distance between Watson–Crick surfaces of opposing uridines (right panel). (e) Conformation of the wobble S34·A(+6) pair in the complex 3 (see Fig. 1c). The absence of two hydrogen bonds expected for the mnm5s2U·A pair can reflect (i) a deformation of the codon–anticodon minihelix induced by the mismatch and (ii) the specific influence of the tRNA modification at position 34 known to counteract misreading of the genetic code. (f) The near-cognate duplex composed of the tRNALysSUU anticodon and the ochre stop codon is significantly weakened compared with the cognate version on the AAA codon with the full set of canonical Watson–Crick interactions. The described weakening of the near-cognate duplex would imply dissociation of tRNALysSUU from the ribosome or, in other terms, rejection.
